<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!--NewPage-->
<HTML>
<HEAD>
<TITLE>
de.hu.berlin.wbi.objects (snp-normalizer)
</TITLE>


<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">

<SCRIPT type="text/javascript">
function windowTitle()
{
    if (location.href.indexOf('is-external=true') == -1) {
        parent.document.title="de.hu.berlin.wbi.objects (snp-normalizer)";
    }
}
</SCRIPT>
<NOSCRIPT>
</NOSCRIPT>

</HEAD>

<BODY BGCOLOR="white" onload="windowTitle();">
<HR>


<!-- ========= START OF TOP NAVBAR ======= -->
<A NAME="navbar_top"><!-- --></A>
<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
<TR>
<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
  <TR ALIGN="center" VALIGN="top">
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>
  </TR>
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
</EM>
</TD>
</TR>

<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
&nbsp;PREV PACKAGE&nbsp;
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/process/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
  <A HREF="../../../../../index.html?de/hu/berlin/wbi/objects/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;
&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
&nbsp;<SCRIPT type="text/javascript">
  <!--
  if(window==top) {
    document.writeln('<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>');
  }
  //-->
</SCRIPT>
<NOSCRIPT>
  <A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>
</NOSCRIPT>


</FONT></TD>
</TR>
</TABLE>
<A NAME="skip-navbar_top"></A>
<!-- ========= END OF TOP NAVBAR ========= -->

<HR>
<H2>
Package de.hu.berlin.wbi.objects
</H2>
Package with the main data objects.
<P>
<B>See:</B>
<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>
<P>

<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
<B>Class Summary</B></FONT></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/DatabaseConnection.html" title="class in de.hu.berlin.wbi.objects">DatabaseConnection</A></B></TD>
<TD>Convenience class for database communication</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A></B></TD>
<TD>Represents a <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/">dbSNP</a>
 entry; loaded from a local database.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A></B></TD>
<TD>Represents a <CODE>Mutation</CODE> mention which has been successfully
 normalized to a <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> .</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A></B></TD>
<TD>Represents the text span of entity mentions (<CODE>Mutation</CODE>, <A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects"><CODE>Gene</CODE></A>, etc.).</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Gene.html" title="class in de.hu.berlin.wbi.objects">Gene</A></B></TD>
<TD>Represents a gene mention found by any Named Enttiy Recognition and Normalization tool.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects">HGVS</A></B></TD>
<TD>Represents a <a href="http://www.hgvs.org/">HGVS</a> reference, like <tt>NR_027062.1:c.157+25766C>T</tt>.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A></B></TD>
<TD>Class to represent a mutation mention found by an NER tool like 
 MutationFinder or SETH</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A></B></TD>
<TD>This object represents a <CODE>Mutation</CODE> from the validation corpus, where
 we already know which <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> entry is associated with this gene.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="../../../../../de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A></B></TD>
<TD>Represents a <a href="www.uniprot.org/">UniProt</a>
 entry; loaded from database.</TD>
</TR>
</TABLE>
&nbsp;

<P>
<A NAME="package_description"><!-- --></A><H2>
Package de.hu.berlin.wbi.objects Description
</H2>

<P>
Package with the main data objects.
<P>

<P>
<DL>
<DT><B>Author:</B></DT>
  <DD>Philippe Thomas</DD>
</DL>
<HR>


<!-- ======= START OF BOTTOM NAVBAR ====== -->
<A NAME="navbar_bottom"><!-- --></A>
<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
<TR>
<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
  <TR ALIGN="center" VALIGN="top">
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>
  </TR>
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
</EM>
</TD>
</TR>

<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
&nbsp;PREV PACKAGE&nbsp;
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/process/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
  <A HREF="../../../../../index.html?de/hu/berlin/wbi/objects/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;
&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
&nbsp;<SCRIPT type="text/javascript">
  <!--
  if(window==top) {
    document.writeln('<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>');
  }
  //-->
</SCRIPT>
<NOSCRIPT>
  <A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>
</NOSCRIPT>


</FONT></TD>
</TR>
</TABLE>
<A NAME="skip-navbar_bottom"></A>
<!-- ======== END OF BOTTOM NAVBAR ======= -->

<HR>

</BODY>
</HTML>
